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- PDB-6tlf: human 14-3-3 sigma isoform in complex with IMP -

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Basic information

Entry
Database: PDB / ID: 6tlf
Titlehuman 14-3-3 sigma isoform in complex with IMP
Components14-3-3 protein sigma
KeywordsSIGNALING PROTEIN / human protein / h14-3-3sigma / complex / inosine monophosphate / IMP
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
INOSINIC ACID / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTassone, G. / Pozzi, C. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Commission675179
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Identification of Phosphate-Containing Compounds as New Inhibitors of 14-3-3/c-Abl Protein-Protein Interaction.
Authors: Iralde-Lorente, L. / Tassone, G. / Clementi, L. / Franci, L. / Munier, C.C. / Cau, Y. / Mori, M. / Chiariello, M. / Angelucci, A. / Perry, M.W.D. / Pozzi, C. / Mangani, S. / Botta, M.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6293
Polymers31,1851
Non-polymers4442
Water39622
1
A: 14-3-3 protein sigma
hetero molecules

A: 14-3-3 protein sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2586
Polymers62,3692
Non-polymers8894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3110 Å2
ΔGint-33 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.294, 100.896, 157.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 31184.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Plasmid: pPROEX-HTb / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40 % wt/vol PEG 4000, 600mM ammonium sulfate, 100 mM Tris-HCl, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.9→84.88 Å / Num. obs: 11508 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1638 / CC1/2: 0.727 / Rrim(I) all: 1.033 / Rsym value: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZ5

1yz5


Resolution: 2.9→78.63 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.867 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.289 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 586 5.1 %RANDOM
Rwork0.2065 ---
obs0.2088 11508 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 192.56 Å2 / Biso mean: 79.065 Å2 / Biso min: 33.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2--0.04 Å20 Å2
3----0.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.4442 Å
Refinement stepCycle: final / Resolution: 2.9→78.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 28 22 1736
Biso mean--149.81 66.91 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121738
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6332353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6565222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20823.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3211510
X-RAY DIFFRACTIONr_chiral_restr0.1480.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021314
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 35 -
Rwork0.329 788 -
all-823 -
obs--100 %

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